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eLife: Repeated origin of gylphosate resistance in waterhemp

Posted on January 17, 2022

Collaboration with Tranel, Stinchcombe and Wright groups, led by Julia Kreiner read more

Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations

Julia Kreiner et al., eLife 11:e70242 (2022). doi: 10.7554/eLife.70242

Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 18 agricultural populations of common waterhemp (Amaranthus tuberculatus), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size (Ne) estimate of 8x107. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median allele age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. The evolutionary history of TSR has also been shaped by both intra- and inter-locus allelic interactions. We report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.

Now in Nature: Essential genes mutate less

Posted on January 12, 2022

Genes subject to stronger purifying selection have a lower mutation rate (OA) read more

Mutation bias reflects natural selection in Arabidopsis thaliana

Grey Monroe et al., Nature, published online January 12, 2022

Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome—mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r?=?0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.

Update on January 23: Altmetric score: top 7% of all Nature articles of similar age. Current Almetric score here.



Again ERC grants for current and former WeigelWorld members

Posted on January 10, 2022

A current and a former postdoc win prestigious ERC Starting Grants read more

Rafal Gutaker, former postdoc with Hernán Burbano and now a group leader at Kew Botanical Gardens, and Derek Lundberg, current postdoc and soon Group Leader at SLU Uppsala, won ERC Starting Grants. Rafal's project GREENrice aims to unlock the properties of pre-Green Revolution rice with focus on nitrogen economy. Derek's SPINOCULANT project has the goal of revealing the secrets to success of Sphingomonas, a versatile bacterial genus with exceptional potential as a beneficial agricultural inoculant. The full list of grantees can be found here. With these two awards, a grand total of 18 ERC grants have been awarded to current and former WeigelWorld members!

Last paper of 2021 in ISME J: Protective Pseudomonas

Posted on December 12, 2021

Local co-existence of pathogenic and protective Pseudomonas lineages read more

Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms

Or Shalev et al., ISME J, published December 11, 2021

Plants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.

A Celebration of Plant Science 2021

Posted on December 10, 2021

International symposium on occasion of Detlef's 60th birthday read more

Current and former members of the Weigel Lab present the "Celebration of Plant Science 2021“, a free International Online Symposium with exceptional line up of speakers, on Dec 16, 2021. More information here.


Derek named a Wallenberg Academy Fellow!

Posted on December 02, 2021

Derek wins Wallenberg Academy Fellowship for his new lab at SLU read more

Wallenberg Academy Fellows, the career program for young researchers launched by the Knut and Alice Wallenberg Foundation in 2012, provides long-term funding for young, promising Swedish and foreign researchers from all academic fields. Derek, who will start his own lab at SLU Uppsala next year, was just named a recipient of this prestigious award. Congratulation, Derek!


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